You can easily backup all your system. Here you have a nice way of doing it
with tar: http://www.aboutdebian.com/tar-backup.htm but you can also use the
backup utility that comes with Trisquel.
You should also burn a live usb / cdrom before you remove the harddisk. Then,
when you have replaced the harddisk, boot from the usb and you could manually
do a repartition of the harddisk and copy everything back. However, I am not
sure if it would make your harddisk bootable.
You could also consider installing Trisquel from the live USB and then
copying everything back. Check if you need to unmount the root partition to
copy everything back. If you need to do so, you can do it from the USB. This
possibility is longer but probably also a bit safer.
